neoscan pipeline v1.3

Pipeline for detecting neoantigen from snvs and indels

Install the third-party software

conda install -c bioconda optitype

Change the path for OptiPathPipeline.py in script neoscan.pl to where you install optitype

Usage

perl neoscan.pl --rdir <rdir> --log <log> --bamfq <bamfq> --bed <bed> --rna <rna> --refdir <refdir> --step <step_number>

    <rdir> = full path of the folder holding files for this sequence run

    <log> = full path of the folder saving log files

    <bamfq> = 1, input is bam; 0, input is fastq: default 1

    <rna> =1, input data is rna, otherwise is dna. For HLA genotype

    <bed> = bed file for annotation: ensembl: /gscmnt/gc2518/dinglab/scao/db/ensembl38.85/proteome-first.bed

     refseq: /gscmnt/gc2518/dinglab/scao/db/refseq_hg38_june29/proteome.bed

    <refdir> = ref directory: /gscmnt/gc2518/dinglab/scao/db/refseq_hg38_june29

    <step_number> run this pipeline step by step. (running the whole pipeline if step number is 0)

files required in the running directory

vcf file format for snvs with columns: chromosome, start position, ref allele, alt allele, gene hugo symbol, HGSV short, is it somatic or germline mutation. Filename: <id>.snp.vcf

 1       113854971       C       G       PTPN22  p.E207Q Somatic

 1       113900168       C       A       AP4B1   p.A284S Somatic

 1       117623561       C       G       FAM46C  p.I231M Somatic

vcf file for indels with the same columns. Filename <id>.indel.vcf

 3       161086280       T       -       B3GALNT1        p.T159Pfs*8     Somatic

RNA-Seq or exome bam or fastq file for HLA type

All three input files should be in one folder. One set of files per sample

Some hints for running neoscan pipleine in WU internal MGI cluster

Copy the tool to a folder. This command will create neoscan/ folder in your current folder:
git clone https://github.com/ding-lab/neoscan.git

This is required to be able to do git checkout, Needed just once:

LSF_DOCKER_PRESERVE_ENVIRONMENT=true bsub -Is -R "select[mem>15000] rusage[mem=15000]" -M 32000000 -q docker-interactive -a "docker(scao/dailybox)" /bin/bash

install optitype

conda install -c bioconda optitype

Change the path for OptiPathPipeline.py in script neoscan.pl to where you install optitype

To prepare vcf and bam input files, you can follow the example at /gscmnt/gc2524/dinglab/akarpova/cptac3/CCRCC_neoscan_test.

perl /gscmnt/gc2524/dinglab/akarpova/software/neoscan/neoscan.pl --rdir /gscmnt/gc2524/dinglab/akarpova/cptac3/CCRCC_neoscan_test --log /gscmnt/gc2524/dinglab/akarpova/cptac3 --bamfq 1 --bed /gscmnt/gc2518/dinglab/scao/db/refseq_hg38_june29/proteome.bed --rna 1 --refdir /gscmnt/gc2518/dinglab/scao/db/refseq_hg38_june29 --step 1

Then change --step 2/3/4/5

After finishing running step 5, you can get the final result in the followint two files:

SAMPLE.neo.snv.summary

SAMPLE.neo.indel.summary

Then you may want to filter out peptides found in human cells in general. Just grep every single peptide in this database /gscmnt/gc2518/dinglab/scao/db/ensembl38.85/Homo_sapiens.GRCh38.pep.all.fa.cleaned.fa

Contact

Song Cao, scao@wustl.edu

Neoscan

Install / Use

README